8.12 EMP_barplot

A bar plot is a statistical chart used to visualize the distribution of data.

8.1.1 Bar Plot for Abundance Data

🏷️Example：

MAE |> 
  EMP_assay_extract('host_gene',pattern = 'A1BG',pattern_ref = 'feature') |>
  EMP_barplot(method='t.test',estimate_group='Group')

8.1.2 Display Only Upper Error Bars

🏷️Example：

MAE |>
  EMP_assay_extract('host_gene',pattern = 'A1BG') |> 
  EMP_barplot(estimate_group = 'Group',error_bar = 'upper')

8.1.3 Subgroup Analysis

🏷️Example：

MAE |>
  EMP_assay_extract('host_gene',pattern = 'A1BG') |> 
  EMP_barplot(estimate_group = 'Group',compare_group='Sex')

8.1.4 Adjusting Statistical Significance Display

🏷️Example：

MAE |>
  EMP_assay_extract('host_gene',pattern = 'ACAD10') |> 
  EMP_barplot(estimate_group = 'Group',label = 'p.signif',label.size=6)

8.1.5 Break the Y axis

🏷️Example：

MAE |>
  EMP_assay_extract('host_gene',pattern = 'ACAD10') |> 
  EMP_barplot(estimate_group = 'Group',label = 'p.signif',
              label.size=6,y_break = c(50,240))

8.1.6 Combining Multiple Features

🏷️Example：

MAE |>
  EMP_assay_extract('host_gene',pattern = 'A1BG') |> 
  EMP_barplot(estimate_group = 'Group',compare_group='Sex',facet = FALSE)

8.1.7 Modifying Comparison Groups

🏷️Example1：Comparing all groups to Group A only

MAE |>
  EMP_assay_extract('host_gene',pattern = 'A1BG') |> 
  EMP_barplot(estimate_group = 'Group',compare_group='sub_group',
              ref.group = 'A',
              facet = FALSE)

🏷️Example2：Comparing only Groups A and B

MAE |>
  EMP_assay_extract('host_gene',pattern = 'A1BG') |> 
  EMP_barplot(estimate_group = 'Group',compare_group='sub_group',
              comparisons = list(c('A','B')),
              facet = FALSE)

8.1.8 Paired Tests

🏷️Example：

MAE |>
  EMP_assay_extract('host_gene',pattern = 'A1BG') |> 
  EMP_barplot(estimate_group = 'sub_group',
              paired_group = 'patient')

8.1.9 Creating GraphPad-Style Plots

🏷️Example1：

Loading the style package:

if (!requireNamespace("ggprism", quietly=TRUE)) install.packages("ggprism")
library(ggprism)

GraphPad uses Tukey's test for multiple group comparisons.

MAE |>
  EMP_assay_extract('host_gene',pattern = 'A1BG') |> 
  EMP_barplot(estimate_group = 'Group',compare_group='Status',
              palette = c('white','red','black'),error_bar = 'upper',
              method = 'tukey.hsd',facet = FALSE,
              mytheme ='theme_prism()')

🏷️Example2：

MAE |>
  EMP_assay_extract('host_gene',pattern = 'A1BG') |> 
  EMP_barplot(estimate_group = 'Group',compare_group='Status',
              bar_alpha = 0,bar_color = 'group',
              palette = c('yellow','red','green'),error_bar = 'upper',
              method = 'tukey.hsd',dot_color = 'group',
              mytheme ='theme_prism()')